New Super Mario Bros. U will get an update to coincide with the release of Super Luigi U, at least in Japan. It will allow players to purchase the Super Luigi U DLC directly from within New Super Mario Bros. U (i.e. no need to visit the eShop), and enable use of the Wii U's Pro Controller.
Director Masataka Takemoto writes on Miiverse that the update is scheduled to arrive with the DLC on June 19. We've contacted Nintendo to see if the update is headed to North America as well.